eelbrain.morph_source_space

eelbrain.morph_source_space(data, subject_to=None, vertices_to=None, morph_mat=None, copy=False, parc=True, xhemi=False, mask=None)

Morph source estimate to a different MRI subject

Parameters
  • data (Union[NDVar, SourceSpace]) – NDVar with SourceSpace dimension.

  • subject_to (Optional[str]) – Name of the subject on which to morph (by default this is the same as the current subject for xhemi morphing).

  • vertices_to (list of array of int | 'lh' | 'rh') – The vertices on the destination subject’s brain. If data contains a whole source space, vertices_to can be automatically loaded, although providing them as argument can speed up processing by a second or two. Use ‘lh’ or ‘rh’ to target vertices from only one hemisphere.

  • morph_mat (Optional[spmatrix]) – The morphing matrix. If data contains a whole source space, the morph matrix can be automatically loaded, although providing a cached matrix can speed up processing by a second or two.

  • copy (bool) – Make sure that the data of morphed_ndvar is separate from data (default False).

  • parc (Union[bool, str]) – Parcellation for target source space. The default is to keep the parcellation from data. Set to False to load no parcellation. If the annotation files are missing for the target subject an IOError is raised.

  • xhemi (bool) – Mirror hemispheres (i.e., project data from the left hemisphere to the right hemisphere and vice versa).

  • mask (Optional[bool]) – Restrict output to known sources. If the parcellation of data is retained keep only sources with labels contained in data, otherwise remove only sourves with ”unknown-*” label (default is True unless vertices_to is specified).

Returns

morphed_ndvar – NDVar morphed to the destination subject.

Return type

NDVar

See also

xhemi

morph data from both hemisphere to one for comparing hemispheres

Notes

This function is used to make sure a number of different NDVars are defined on the same MRI subject and handles scaled MRIs efficiently. If the MRI subject on which data is defined is a scaled copy of subject_to, by default a shallow copy of data is returned. That means that it is not safe to assume that morphed_ndvar can be modified in place without altering data. To make sure the date of the output is independent from the data of the input, set the argument copy=True.

Examples

Generate a symmetric ROI based on a test result (res):

# Generate a mask based on significance
mask = res.p.min('time') <= 0.05
# store the vertices for which we want the end result
fsa_vertices = mask.source.vertices
# morphing is easier with a complete source space
mask = complete_source_space(mask)
# Use a parcellation that is available for the ``fsaverage_sym`` brain
mask = set_parc(mask, 'aparc')
# morph both hemispheres to the left hemisphere
mask_from_lh, mask_from_rh = xhemi(mask)
# take the union; morphing interpolates, so re-cast values to booleans
mask_lh = (mask_from_lh > 0) | (mask_from_rh > 0)
# morph the new ROI to the right hemisphere
mask_rh = morph_source_space(mask_lh, vertices_to=[[], mask_lh.source.vertices[0]], xhemi=True)
# cast back to boolean
mask_rh = mask_rh > 0
# combine the two hemispheres
mask_sym = concatenate([mask_lh, mask_rh], 'source')
# morph the result back to the source brain (fsaverage)
mask = morph_source_space(mask_sym, 'fsaverage', fsa_vertices)
# convert to boolean mask (morphing involves interpolation, so the output is in floats)
mask = round(mask).astype(bool)